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clinvar-variation-skill

Search ClinVar and NCBI Variation for genetic variants, or look up records using VCV, RCV, SCV, and RefSNP identifiers. Get concise summaries, check identifier mappings, and save full JSON responses when needed.

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原文查看原文说明

Submit compact ClinVar Clinical Tables and NCBI Variation requests for search, VCV, RCV, SCV, and RefSNP lookups. Use when a user wants variant-level summaries or identifier mapping

查看安装方法

适用场景

  • Searching ClinVar for a genetic variant
  • Looking up VCV, RCV, SCV, or RefSNP records
  • Checking mappings between variant identifiers
  • Saving full responses as JSON files

包含的文件(3)

  • SKILL.md2.0 KB
  • agents/openai.yaml120 B
  • scripts/clinvar_variation.py7.7 KB

SKILL.md(原文)

安装前可以查看交给 AI 代理的指令内容。

Operating rules

  • Use scripts/clinvar_variation.py for all ClinVar and NCBI Variation work.
  • The script accepts max_items; for action=search, start around max_items=10.
  • For vcv, rcv, scv, and refsnp, omit max_items unless you need to trim nested arrays in the summary.
  • Re-run requests in long conversations instead of relying on prior tool output.
  • Treat displayed ... in tool previews as UI truncation, not literal request content.
  • If the user asks for full JSON, set save_raw=true and report the saved file path instead of pasting large payloads into chat.

Execution behavior

  • Return concise markdown summaries from the script JSON by default.
  • Return the JSON verbatim only if the user explicitly asks for machine-readable output.
  • Use action=search for the Clinical Tables endpoint.
  • Use action=vcv|rcv|scv|refsnp for NCBI Variation beta objects.

Input

  • Read one JSON object from stdin.
  • Required field: action
  • Action-specific required fields:
    • search: terms
    • vcv: vcv
    • rcv: rcv
    • scv: scv
    • refsnp: refsnp
  • Optional fields: params, max_items, max_depth, timeout_sec, save_raw, raw_output_path

Output

  • search returns total, identifiers, display_rows, extra_fields, and truncation metadata.
  • vcv|rcv|scv|refsnp return a compact summary and optional top_keys.
  • Use raw_output_path when save_raw=true.
  • Failures return ok=false with error.code and error.message.

Execution

echo '{"action":"search","terms":"VCV000013080","max_items":10}' | python scripts/clinvar_variation.py

References

  • No additional runtime references are required; keep the import package limited to this file and scripts/clinvar_variation.py.

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